His work with the character continued into late 2003, furthering his love of the crime genre and culminating in the noir masterpiece Gotham Central, brought to visual reality by the pencils of Michael Lark and co-written with Rucka. Given Batman as his first subject, he found his crime style more than a match for the world's greatest detective. This flavour has appealed to the editors of some of DC and Marvel's more street-level titles, and Brubaker subsequently found himself working in years to come alongside writers Greg Rucka, Brian Michael Bendis, and Matt Fraction to develop some of comics most beloved icons. The Mainstreamīrubaker is known for applying a crime-fiction style to his comics writing.

Together they created the four-issue limited series Scene of the Crime, landing Brubaker his second and third Eisner nominations.The following year he signed his first exclusive contract (with DC) and began his first work on Batman. Further work under the Vertigo label in 1999 partnered Brubaker for the first time with Michael Lark and Sean Phillips. The series never continued, despite having garnered him an Harvey Award nomination for Best New Series. They published the first issue of his proposed experimental series Detour that year, but never more than that. In 1997 he approached Alternative Comics with his cartooning work. Collaborating with Shanower again in '95 Brubaker wrote Prez: Smells Like Teen President, a satirical piece published by the DC imprint Vertigo for mature readers. Brubaker continued to write for the serial throughout the decade, even as his career took him to greater heights.

Collaborating with artist Eric Shanower he wrote the three-issue story arc An Accidental Death (Dark Horse Presents #65-67), earning the two creators a 1993 Eisner Award nomination. In 1991 he started writing his semi-autobiographical series Lowlife for Caliber Comics and submitting crime fiction stories to Dark Horse Comics for their Dark Horse Presents serial. Launching into the comics industry as a cartoonist, Brubaker spent the late 1980s writing and drawing for Blackthorne Comics and Slave Labour Graphics.

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